import pandas as pd
import numpy as np 
import matplotlib.pyplot as plt
# import seaborn as sns 
import datetime
from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
from plotly.graph_objs import Scatter, Figure, Layout
import plotly
import plotly.graph_objs as go
import plotly.express as px
from IPython.display import Markdown as md
init_notebook_mode(connected=False)
import io
import requests
import re

COVID-19 in Italy. Visuals

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(alternatively, see results and code together here)

 

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Data source: this GitHubi page

Authors and sources mentioned: Editore/Autore del dataset: Dipartimento della Protezione Civile. Categoria ISO 19115: Salute. Dati forniti dal Ministero della Salute.

Regional data files (Dati per Regione):

• Struttura file giornaliero: dpc-covid19-ita-regioni-yyyymmdd.csv (dpc-covid19-ita-regioni-20200224.csv)
• File complessivo: dpc-covid19-ita-regioni.csv
• File ultimi dati (latest): dpc-covid19-ita-regioni-latest.csv

 

• Below we use the 'dpc-covid19-ita-regioni.csv' file (updated on daily basis, so far).

• In addition, we get regional population size from https://it.wikipedia.org/wiki/Regione_(Italia) for per capita measures

URL='https://it.wikipedia.org/wiki/Regione_(Italia)'
res=requests.get(URL)
tables=pd.read_html(res.text)
dt = tables[13]

def dewhite(x):
    ''.join(re.findall('\d+', x))

dt2 = dt[['Regione','Popolazione (ab.)']].copy()
dt2.columns = ['Region','Pop']
    
dt2.Pop = dt2.Pop.apply(lambda x: ''.join(re.findall('\d+', x))).astype(int)

s = requests.get("https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv").content
dat = pd.read_csv(io.StringIO(s.decode('utf-8')))
cdate = dat.data.max()

md("Currently data as of date: {}".format(cdate))

Currently data as of date: 2021-05-05T17:00:00

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What's in the original dataframe?

md("All column names: {}".format(dat.columns.tolist()))

All column names: ['data', 'stato', 'codice_regione', 'denominazione_regione', 'lat', 'long', 'ricoverati_con_sintomi', 'terapia_intensiva', 'totale_ospedalizzati', 'isolamento_domiciliare', 'totale_positivi', 'variazione_totale_positivi', 'nuovi_positivi', 'dimessi_guariti', 'deceduti', 'casi_da_sospetto_diagnostico', 'casi_da_screening', 'totale_casi', 'tamponi', 'casi_testati', 'note', 'ingressi_terapia_intensiva', 'note_test', 'note_casi', 'totale_positivi_test_molecolare', 'totale_positivi_test_antigenico_rapido', 'tamponi_test_molecolare', 'tamponi_test_antigenico_rapido', 'codice_nuts_1', 'codice_nuts_2']

df = dat.drop(['stato','codice_regione'], axis=1)
df.columns = ['Date','Region','Lat','Long','HospWithSymptoms','IC','HospTotal','AtHome','CurrentlyPositive','VariationOfPositives','NewPositives','Recovered', 'Deaths','Diagnostico','Screening','TotalCases','NoOfTests','casi_testati','note','ingr_ter_intens','note_test','note_casi', 'totale_positivi_test_molecolare', 'totale_positivi_test_antigenico_rapido', 'tamponi_test_molecolare', 'tamponi_test_antigenico_rapido', 'codice_nuts_1', 'codice_nuts_2']

df = pd.merge(df, dt2, left_on='Region', right_on='Region')

df['Date'] = pd.to_datetime(df['Date']).dt.date
df = df.set_index(df["Date"])
df.index = pd.to_datetime(df.index)

df['NewPositives'] = np.abs(df['NewPositives'])

dat.tail(5)

	data	stato	codice_regione	denominazione_regione	lat	long	ricoverati_con_sintomi	terapia_intensiva	totale_ospedalizzati	isolamento_domiciliare	...	note	ingressi_terapia_intensiva	note_test	note_casi	totale_positivi_test_molecolare	totale_positivi_test_antigenico_rapido	tamponi_test_molecolare	tamponi_test_antigenico_rapido	codice_nuts_1	codice_nuts_2
9172	2021-05-05T17:00:00	ITA	19	Sicilia	38.115697	13.362357	1121	152	1273	23256	...	NaN	7.0	NaN	NaN	212677.0	0.0	2323160.0	1681158.0	ITG	ITG1
9173	2021-05-05T17:00:00	ITA	9	Toscana	43.769231	11.255889	1218	229	1447	17489	...	NaN	17.0	NaN	NaN	227254.0	3030.0	3384070.0	841809.0	ITI	ITI1
9174	2021-05-05T17:00:00	ITA	10	Umbria	43.106758	12.388247	146	24	170	2557	...	Si fa presente che 4 dei ricoveri NON UTI, non...	0.0	NaN	NaN	54867.0	0.0	870527.0	325485.0	ITI	ITI2
9175	2021-05-05T17:00:00	ITA	2	Valle d'Aosta	45.737503	7.320149	37	9	46	584	...	NaN	2.0	NaN	NaN	10517.0	561.0	91484.0	25187.0	ITC	ITC2
9176	2021-05-05T17:00:00	ITA	5	Veneto	45.434905	12.338452	854	145	999	19177	...	NaN	12.0	NaN	NaN	403605.0	11367.0	5068508.0	2203790.0	ITH	ITH3

5 rows × 30 columns

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Variable names to English and their explanation

• HospWithSymptoms : Currently hospitalized patients with symptoms
• IC : Intensive care
• HospTotal: Total number of currently hospitalized patients
• AtHome : Currently at home confinement
• CurrentlyPositive : Total amount of current positive cases (Hospitalised patients + Home confinement)
• NewPositives : New amount of positive cases (Actual total amount of current positive cases - total amount of current positive cases of the previous day)
• TotalCases : Total amount of positive cases
• NoOfTests : Tests performed

df.tail()

	Date	Region	Lat	Long	HospWithSymptoms	IC	HospTotal	AtHome	CurrentlyPositive	VariationOfPositives	...	ingr_ter_intens	note_test	note_casi	totale_positivi_test_molecolare	totale_positivi_test_antigenico_rapido	tamponi_test_molecolare	tamponi_test_antigenico_rapido	codice_nuts_1	codice_nuts_2	Pop
Date
2021-05-01	2021-05-01	Veneto	45.434905	12.338452	907	154	1061	20715	21776	-116	...	14.0	NaN	NaN	401663.0	11150.0	5020063.0	2156665.0	ITH	ITH3	4879133
2021-05-02	2021-05-02	Veneto	45.434905	12.338452	897	149	1046	20694	21740	-36	...	5.0	NaN	NaN	402044.0	11098.0	5030579.0	2160961.0	ITH	ITH3	4879133
2021-05-03	2021-05-03	Veneto	45.434905	12.338452	896	151	1047	20876	21923	183	...	4.0	NaN	NaN	402415.0	11091.0	5037578.0	2163499.0	ITH	ITH3	4879133
2021-05-04	2021-05-04	Veneto	45.434905	12.338452	878	149	1027	19987	21014	-909	...	14.0	NaN	NaN	402935.0	11292.0	5050898.0	2184563.0	ITH	ITH3	4879133
2021-05-05	2021-05-05	Veneto	45.434905	12.338452	854	145	999	19177	20176	-838	...	12.0	NaN	NaN	403605.0	11367.0	5068508.0	2203790.0	ITH	ITH3	4879133

5 rows × 29 columns

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Regional trends

daily numbers & moving averages (MA)

(Tip: double click and click on legend to select one or multiple regions in graphs)

df2 = df

fig = px.line(df2, x="Date", y="NewPositives", color="Region", hover_name="Region",
        render_mode="svg", log_y=False)
fig.update_layout(title="Daily new positive cases")
fig.show()

df2['MovAv7'] = df2['NewPositives'].rolling(window=7).mean()

fig = px.line(df2[df2.index>'2020-3-1'], x="Date", y="MovAv7", color="Region", hover_name="Region",
        render_mode="svg", log_y=False)
fig.update_layout(title="7-day MA of new positive cases")
fig.show()

df2['NewPos_per_100K'] = df2['NewPositives']/df2['Pop']*1000_00

df2['NewPos_per_100K'] = df2['NewPos_per_100K'].rolling(window=7).mean()

fig = px.line(df2[df2.index>'2020-3-1'], x="Date", y="NewPos_per_100K", color="Region", 
              hover_name="Region", log_y=False)
fig.update_layout(title="7-day MA of new positive cases, per 100K")
fig.show()

df2['PosTests'] = df2['NewPositives']/df2['NoOfTests']*100

fig = px.scatter(df2, y="PosTests", x="Date", color="Region", 
              hover_name="Region", log_y=True)
fig.update_layout(title="Percentage of positive tests")
fig.show()

df2['IC_per_100K'] = df2['IC']/df2['Pop']*1000_00

fig = px.line(df2, x="Date", y="IC_per_100K", color="Region", hover_name="Region",
        render_mode="svg", log_y=False)
fig.update_layout(title="Current number of intensive care patients, per 100K")
fig.show()

df2['Hosp_per_100K'] = df2['HospTotal']/df2['Pop']*1000_00

fig = px.line(df2, x="Date", y="Hosp_per_100K", color="Region", hover_name="Region",
        render_mode="svg", log_y=False)
fig.update_layout(title="Current number of hospitalized, per 100K")
fig.show()

df3 = df2.copy()

df3['NewDeaths'] = df3['Deaths'] - df3.groupby(['Region'])['Deaths'].transform('shift')

fig = px.bar(df3, x=df3['Date'], y="NewDeaths", color="Region", hover_name="Date")
fig.update_layout(title="Daily number of deaths")
fig.show()

df2['Deaths_per_100K'] = (df2['Deaths']/df2['Pop'])*1000_00
fig = px.line(df2, x="Date", y="Deaths_per_100K", color="Region", 
              hover_name="Region", render_mode="svg", line_shape='spline')
fig.update_layout(title="Cumulative number of deaths, per 100K")
fig.show()

df2['Change_per_100K'] = df2['VariationOfPositives']/df2['Pop']*1000_00
df2['Change_per_100K'] = df2['Change_per_100K'].rolling(window=7).mean()

fig = px.line(df2[(df2.index>'2020-3-1') & (df2['Region']!="""Valle d'Aosta""")], x='Date', y="Change_per_100K", 
              color="Region", hover_name="Date")
fig.update_layout(title="7-day MA of change in current positive cases, per 100K (excl. Valle d'Aosta)")
fig.show()

df2['Current_per_100K'] = df2['CurrentlyPositive']/df2['Pop']*1000_00
df2['Current_per_100K'] = df2['Current_per_100K'].rolling(window=14).mean()

fig = px.line(df2[(df2.index>'2020-3-7')], x='Date', y="Current_per_100K", color="Region", hover_name="Date")
fig.update_layout(title="14-day MA of current positive cases, per 100K")
fig.show()

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All regions together

df2 = df
df_sum = df2.drop(['Lat','Long'], axis=1).groupby(df.Date).sum().reset_index()

df_sum2 = pd.melt(df_sum, id_vars=['Date'], value_vars=['NewPositives','IC','HospTotal','CurrentlyPositive'])

fig = px.line(df_sum2, x="Date", y="value", color='variable', hover_name="value", render_mode="svg", log_y=True, 
              line_shape='spline')
fig.update_layout(title="Number of new and current positives, current IC patients and currently hospitalized")
fig.show()

Molecular test positive rate

df2['pos.test.rate.mol'] = df2['totale_positivi_test_molecolare']/df2['tamponi_test_molecolare']*100


fig = px.line(df2[(df2.index>'2021-1-10') & (df2['Region']!="""Valle d'Aosta""")], x='Date', y="pos.test.rate.mol", 
              color="Region", hover_name="Date")
fig.update_layout(title="7-day MA of change in current positive cases, per 100K (excl. Valle d'Aosta)")
fig.show()

Antigene test positive rate

df2['pos.test.rate.ant'] = df2['totale_positivi_test_antigenico_rapido']/df2['tamponi_test_antigenico_rapido']*100


fig = px.line(df2[(df2.index>'2021-1-10') & (df2['Region']!="""Valle d'Aosta""")], x='Date', y="pos.test.rate.ant", 
              color="Region", hover_name="Date")
fig.update_layout(title="7-day MA of change in current positive cases, per 100K (excl. Valle d'Aosta)")
fig.show()